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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ), 'gf_id' => 'HOM05D001114', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001114' ), 'data_identifier' => 'HOM05D001114', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001114', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p01330' => 'bna', 'A01p07310' => 'bna', 'A02p06140' => 'bna', 'A03p09980' => 'bna', 'A03p27220' => 'bna', 'A03p60390' => 'bna', 'A03p65460' => 'bna', 'A09p56500' => 'bna', 'A10p19670' => 'bna', 'Aa31LG1G14350' => 'aar', 'Aa31LG6G14580' => 'aar', 'Aa31LG7G12620' => 'aar', 'Aa31LG7G12630' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2702' => 'aag', 'Actinidia10208' => 'ach', 'Actinidia11976' => 'ach', 'Actinidia21942' => 'ach', 'Actinidia26605' => 'ach', 'Actinidia32843' => 'ach', 'Actinidia33301' => 'ach', 'Ah.03g140590' => 'amhyb', 'Ah.05g167040' => 'amhyb', 'Ah.09g224280' => 'amhyb', 'Ah.09g228650' => 'amhyb', 'Ah.14g079280' => 'amhyb', 'AL4G14270' => 'aly', 'AL4G45570' => 'aly', 'AL6G31820' => 'aly', 'AL7G11550' => 'aly', 'AL7G13090' => 'aly', 'AL7G21260' => 'aly', 'Aqoxy6G02565' => 'aox', 'Aqoxy7G02416' => 'aox', 'Aqoxy7G03295' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0EU6RV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.14IIV2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ALJH5D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L6NNIX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N37HAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SP0UUF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T4QRY3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TJMK61' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN5GN2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X02P63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YK8V62' => 'arhy', 'AT2G24150' => 'ath', 'AT2G40710' => 'ath', 'AT4G30850' => 'ath', 'AT4G37680' => 'ath', 'AT4G38290' => 'ath', 'AT4G38320' => 'ath', 'AT4G38330' => 'ath', 'AT5G20270' => 'ath', 'ATR0580G407' => 'atr', 'ATR0739G029' => 'atr', 'ATR0767G034' => 'atr', 'Atru.chr13.846' => 'acertr', 'Atru.chr3.1030' => 'acertr', 'Atru.chr7.1962' => 'acertr', 'Atru.chr7.384' => 'acertr', 'AUR62004021' => 'cqu', 'AUR62007529' => 'cqu', 'AUR62011190' => 'cqu', 'AUR62013296' => 'cqu', 'AUR62022467' => 'cqu', 'AUR62025376' => 'cqu', 'AUR62025377' => 'cqu', 'AUR62028374' => 'cqu', 'AUR62028375' => 'cqu', 'AUR62041659' => 'cqu', 'BcaB01g02984' => 'bca', 'BcaB01g04794' => 'bca', 'BcaB05g22855' => 'bca', 'BcaB08g36533' => 'bca', 'BcaC01g04878' => 'bca', 'BcaC03g13747' => 'bca', 'BcaC04g19417' => 'bca', 'BcaC04g19418' => 'bca', 'BcaC07g40955' => 'bca', 'BcaC09g51870' => 'bca', 'BcaC09g51874' => 'bca', 'BcaNung01555' => 'bca', 'BcaNung02079' => 'bca', 'BcaNung02081' => 'bca', 'BcaNung02734' => 'bca', 'BcaNung03434' => 'bca', 'BcaNung05785' => 'bca', 'BcaNung05786' => 'bca', 'BcaNung05787' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01700' => 'bna', 'BolC1t00146H' => 'bol', 'BolC1t00796H' => 'bol', 'BolC2t07031H' => 'bol', 'BolC3t13626H' => 'bol', 'BolC3t15607H' => 'bol', 'BolC7t46284H' => 'bol', 'BolC7t46671H' => 'bol', 'BolC8t51521H' => 'bol', 'BolC9t58461H' => 'bol', 'BraA01t00130Z' => 'bra', 'BraA01t00680Z' => 'bra', 'BraA02t05564Z' => 'bra', 'BraA03t10309Z' => 'bra', 'BraA03t11935Z' => 'bra', 'BraA03t15079Z' => 'bra', 'BraA03t15598Z' => 'bra', 'BraA09t41043Z' => 'bra', 'BraA10t44042Z' => 'bra', 'C01p01490' => 'bna', 'C01p08070' => 'bna', 'C03p11540' => 'bna', 'C03p32710' => 'bna', 'C07p58260' => 'bna', 'C07p62560' => 'bna', 'C08p39470' => 'bna', 'C09p55930' => 'bna', 'CAN.G1075.47' => 'can', 'CAN.G1190.20' => 'can', 'CAN.G153.1' => 'can', 'CAN.G153.2' => 'can', 'CAN.G153.3' => 'can', 'CAN.G153.4' => 'can', 'CAN.G551.17' => 'can', 'CAN.G551.77' => 'can', 'CAN.G980.17' => 'can', 'CANSAT01G0260' => 'cansat', 'CANSAT11G0535' => 'cansat', 'CANSAT11G2420' => 'cansat', 'CARHR118140' => 'chi', 'CARHR192560' => 'chi', 'CARHR238710' => 'chi', 'CARHR246060' => 'chi', 'Carub.0004s0333' => 'cru', 'Carub.0006s1866' => 'cru', 'Carub.0007s0259' => 'cru', 'Carub.0007s0970' => 'cru', 'Ca_13263_v3' => 'car', 'Ca_15898_v3' => 'car', 'Ca_21663_v3' => 'car', 'Ca_24679_v3' => 'car', 'CBR_g12080' => 'cbr', 'Cc06_g07920' => 'ccan', 'Cc06_g07930' => 'ccan', 'Cc06_g10690' => 'ccan', 'Cc06_g14460' => 'ccan', 'Cc07_g07200' => 'ccan', 'CDE02G4353' => 'cde', 'CDE04G2644' => 'cde', 'CDE05G0076' => 'cde', 'CDE05G0904' => 'cde', 'CDE05G1787' => 'cde', 'CDE05G1854' => 'cde', 'CDE06G2762' => 'cde', 'Cfa013763' => 'cfa', 'Cfa020778' => 'cfa', 'Cfa024171' => 'cfa', 'Cfa026299' => 'cfa', 'Ciclev10001488m.g' => 'ccl', 'Ciclev10008677m.g' => 'ccl', 'Ciclev10025731m.g' => 'ccl', 'CiPaw.01G003300' => 'cil', 'CiPaw.03G249500' => 'cil', 'CiPaw.04G175900' => 'cil', 'CiPaw.08G050700' => 'cil', 'CiPaw.15G163900' => 'cil', 'CiPaw.16G106400' => 'cil', 'ClCG01G017680' => 'cla', 'ClCG06G011610' => 'cla', 'ClCG06G012680' => 'cla', 'COL.COLO4_11592' => 'col', 'COL.COLO4_36573' => 'col', 'Cpa.g.sc142.40' => 'cpa', 'Cpa.g.sc199.11' => 'cpa', 'Cpa.g.sc46.56' => 'cpa', 'Cpa.g.sc6.2' => 'cpa', 'Cre06.g303900' => 'cre', 'CsaV3_1G027960' => 'csa', 'CsaV3_1G029230' => 'csa', 'CsaV3_6G044210' => 'csa', 'CSS0006963' => 'camsi', 'CSS0010744' => 'camsi', 'CSS0018597' => 'camsi', 'CSS0018808' => 'camsi', 'CSS0024100' => 'camsi', 'CSS0030475' => 'camsi', 'CSS0030815' => 'camsi', 'CSS0031552' => 'camsi', 'CSS0045614' => 'camsi', 'CSS0049399' => 'camsi', 'DCAR_014800' => 'dca', 'DCAR_014904' => 'dca', 'DCAR_017777' => 'dca', 'DCAR_021463' => 'dca', 'DCAR_021464' => 'dca', 'DCAR_024621' => 'dca', 'Dinv36472' => 'din', 'Dinv41338' => 'din', 'Dinv41467' => 'din', 'Dinv42814' => 'din', 'Dinv43286' => 'din', 'Dinv44945' => 'din', 'Duzib147G0936' => 'dzi', 'Duzib150G0423' => 'dzi', 'Duzib168G0925' => 'dzi', 'Duzib168G1046' => 'dzi', 'Duzib187G0373' => 'dzi', 'Duzib187G1032' => 'dzi', 'Duzib187G1244' => 'dzi', 'Duzib264G0544' => 'dzi', 'ECA234G4449' => 'eca', 'ECA236G0517' => 'eca', 'ECA236G0919' => 'eca', 'ECA236G3791' => 'eca', 'ECA246G4652' => 'eca', 'EL10Ac1g02366' => 'bvu', 'EL10Ac6g15609' => 'bvu', 'EL10Ac8g18748' => 'bvu', 'EL10Ac8g18903' => 'bvu', 'Eucgr.C02517' => 'egr', 'Eucgr.C04293' => 'egr', 'Eucgr.C04304' => 'egr', 'Eucgr.C04315' => 'egr', 'Eucgr.C04321' => 'egr', 'Eucgr.F00055' => 'egr', 'Eucgr.F00059' => 'egr', 'Eucgr.F00063' => 'egr', 'Eucgr.F00065' => 'egr', 'Eucgr.I00694' => 'egr', 'Eucgr.L01550' => 'egr', 'FAN07G1385' => 'fan', 'FAN08G2233' => 'fan', 'FAN13G0654' => 'fan', 'FAN13G1119' => 'fan', 'FAN17G1941' => 'fan', 'FAN18G4086' => 'fan', 'FAN19G2658' => 'fan', 'FAN19G2690' => 'fan', 'FAN22G0358' => 'fan', 'FAN23G0214' => 'fan', 'FAN23G2663' => 'fan', 'FAN26G1794' => 'fan', 'FAN26G2805' => 'fan', 'FAN28G0606' => 'fan', 'FAN28G1432' => 'fan', 'FvH4_1g02500' => 'fve', 'FvH4_1g17920' => 'fve', 'FvH4_4g08550' => 'fve', 'FvH4_5g20320' => 'fve', 'FvH4_6g47370' => 'fve', 'Glyma.01G194900' => 'gma', 'Glyma.02G207000' => 'gma', 'Glyma.04G046500' => 'gma', 'Glyma.04G156100' => 'gma', 'Glyma.06G047200' => 'gma', 'Glyma.06G223600' => 'gma', 'Glyma.11G046900' => 'gma', 'Glyma.13G161500' => 'gma', 'Glyma.17G070900' => 'gma', 'Glyma.17G109800' => 'gma', 'Gohir.A02G150700' => 'ghi', 'Gohir.A06G053200' => 'ghi', 'Gohir.A08G087700' => 'ghi', 'Gohir.A11G048700' => 'ghi', 'Gohir.A11G213900' => 'ghi', 'Gohir.A13G101510' => 'ghi', 'Gohir.A13G201000' => 'ghi', 'Gohir.A13G201100' => 'ghi', 'Gohir.D03G029700' => 'ghi', 'Gohir.D06G052200' => 'ghi', 'Gohir.D08G098800' => 'ghi', 'Gohir.D11G052300' => 'ghi', 'Gohir.D11G209500' => 'ghi', 'Gohir.D13G206700' => 'ghi', 'Gohir.D13G206800' => 'ghi', 'Gorai.003G031300' => 'gra', 'Gorai.004G106400' => 'gra', 'Gorai.007G056700' => 'gra', 'Gorai.007G224700' => 'gra', 'Gorai.010G060500' => 'gra', 'Gorai.013G235700' => 'gra', 'Gorai.013G235800' => 'gra', 'GSVIVG01006023001' => 'vvi', 'GSVIVG01009324001' => 'vvi', 'GSVIVG01012821001' => 'vvi', 'GSVIVG01023696001' => 'vvi', 'HanXRQChr05g0143861' => 'han', 'HanXRQChr05g0143871' => 'han', 'HanXRQChr06g0179771' => 'han', 'HanXRQChr09g0264501' => 'han', 'HanXRQChr10g0315381' => 'han', 'HanXRQChr15g0472581' => 'han', 'Haze_15270' => 'cav', 'Haze_19118' => 'cav', 'Haze_19122' => 'cav', 'Haze_22420' => 'cav', 'Haze_25486' => 'cav', 'Haze_26497' => 'cav', 'Hma1.2p1_0852F.1_g228650' => 'hma', 'Hma1.2p1_1084F.1_g255340' => 'hma', 'HPP92_003662' => 'vpl', 'HPP92_003665' => 'vpl', 'HPP92_003852' => 'vpl', 'HPP92_013385' => 'vpl', 'HPP92_013405' => 'vpl', 'HPP92_020612' => 'vpl', 'Hund08955' => 'sun', 'Hund09292' => 'sun', 'Hund16408' => 'sun', 'Hund21571' => 'sun', 'Hund31317' => 'sun', 'Lalb_Chr05g0213761' => 'lal', 'Lalb_Chr07g0179311' => 'lal', 'Lalb_Chr11g0072481' => 'lal', 'Lalb_Chr12g0198271' => 'lal', 'Lalb_Chr13g0300661' => 'lal', 'Lalb_Chr16g0378931' => 'lal', 'Lj1g0021795' => 'lja', 'Lj2g0017513' => 'lja', 'Lj4A163T74' => 'lonja', 'Lj4A72T41' => 'lonja', 'Lj4g0005704' => 'lja', 'Lj6g0024092' => 'lja', 'Lj7A109T43' => 'lonja', 'Lj7A436T63' => 'lonja', 'Lj7A464T43' => 'lonja', 'Lsat_1_v5_gn_3_86641' => 'lsa', 'Lsat_1_v5_gn_4_107041' => 'lsa', 'Lsat_1_v5_gn_5_93720' => 'lsa', 'Lsat_1_v5_gn_8_61081' => 'lsa', 'Lsat_1_v5_gn_8_61480' => 'lsa', 'Lsat_1_v5_gn_8_64861' => 'lsa', 'Manes.05G182500' => 'mes', 'Manes.06G032300' => 'mes', 'Manes.06G045900' => 'mes', 'Manes.12G115900' => 'mes', 'Manes.13G110400' => 'mes', 'Manes.14G116900' => 'mes', 'Mapoly0001s0183' => 'mpo', 'Mapoly0021s0058' => 'mpo', 'Mapoly0077s0057' => 'mpo', 'Mapoly0077s0059' => 'mpo', 'MBI14_g16443_MAGBIO' => 'mbi', 'MBI15_g00260_MAGBIO' => 'mbi', 'MBI15_g00261_MAGBIO' => 'mbi', 'MBI15_g41308_MAGBIO' => 'mbi', 'MBI16_g18974_MAGBIO' => 'mbi', 'MCO12G198' => 'mco', 'MD02G1022400' => 'mdo', 'MD02G1187800' => 'mdo', 'MD04G1052800' => 'mdo', 'MD04G1053000' => 'mdo', 'MD06G1047400' => 'mdo', 'MD15G1165000' => 'mdo', 'MD15G1165100' => 'mdo', 'MD15G1298700' => 'mdo', 'MD15G1444500' => 'mdo', 'Medtr0066s0040' => 'mtr', 'Medtr0066s0050' => 'mtr', 'Medtr3g103240' => 'mtr', 'Medtr4g115580' => 'mtr', 'Medtr5g015270' => 'mtr', 'MELO3C007646.2' => 'cme', 'MELO3C010196.2' => 'cme', 'MELO3C010301.2' => 'cme', 'Migut.H00338' => 'egut', 'Migut.J01205' => 'egut', 'Migut.K00299' => 'egut', 'Migut.K00419' => 'egut', 'MSTRG.10656' => 'ama', 'MSTRG.19665' => 'ama', 'MSTRG.23664' => 'ama', 'MSTRG.2816' => 'ama', 'MSTRG.6165' => 'ama', 'Nitab4.5_0000142g0240' => 'nta', 'Nitab4.5_0001417g0020' => 'nta', 'Nitab4.5_0001751g0160' => 'nta', 'Nitab4.5_0002659g0060' => 'nta', 'Nitab4.5_0002809g0010' => 'nta', 'Nitab4.5_0003129g0010' => 'nta', 'Nitab4.5_0003759g0030' => 'nta', 'Nitab4.5_0005159g0040' => 'nta', 'Nitab4.5_0006696g0040' => 'nta', 'Nitab4.5_0007023g0020' => 'nta', 'Nitab4.5_0007023g0030' => 'nta', 'Nitab4.5_0007330g0030' => 'nta', 'Nn1g04514' => 'nnu', 'Nn2g12132' => 'nnu', 'Nn2g12729' => 'nnu', 'Nn5g30624' => 'nnu', 'Nn8g39574' => 'nnu', 'Oeu000516.1' => 'oeu', 'Oeu010280.1' => 'oeu', 'Oeu011984.1' => 'oeu', 'Oeu013331.1' => 'oeu', 'Oeu014255.2' => 'oeu', 'Oeu032427.1' => 'oeu', 'Oeu034736.2' => 'oeu', 'Oeu055959.1' => 'oeu', 'Os02g0179500' => 'osa', 'Os03g0200000' => 'osa', 'Os03g0232900' => 'osa', 'Os03g0432200' => 'osa', 'Os06g0643700' => 'osa', 'Os06g0652200' => 'osa', 'Os12g0511200' => 'osa', 'Peaxi162Scf00005g00612' => 'pax', 'Peaxi162Scf00038g00721' => 'pax', 'Peaxi162Scf00088g01218' => 'pax', 'Peaxi162Scf00108g00313' => 'pax', 'Peaxi162Scf00118g01712' => 'pax', 'Peaxi162Scf00548g00226' => 'pax', 'PGR004G0920' => 'pgr', 'PGR102G1822' => 'pgr', 'PGR102G2203' => 'pgr', 'PGSC0003DMG400002879' => 'stu', 'PGSC0003DMG400007818' => 'stu', 'PGSC0003DMG400009091' => 'stu', 'PGSC0003DMG400011156' => 'stu', 'PGSC0003DMG400021438' => 'stu', 'PGSC0003DMG400027937' => 'stu', 'Phvul.002G010000' => 'pvu', 'Phvul.003G153200' => 'pvu', 'Phvul.003G170000' => 'pvu', 'Phvul.004G109600' => 'pvu', 'Phvul.009G072600' => 'pvu', 'Phvul.009G195500' => 'pvu', 'Potri.006G064400' => 'ptr', 'Potri.007G005800' => 'ptr', 'Potri.014G006000' => 'ptr', 'Potri.018G102400' => 'ptr', 'Potri.018G124754' => 'ptr', 'Potri.T124407' => 'ptr', 'Pp3c14_14690' => 'ppa', 'Pp3c15_17020' => 'ppa', 'Pp3c1_29610' => 'ppa', 'Pp3c2_17690' => 'ppa', 'Pp3c9_10980' => 'ppa', 'PRCOL_00001358' => 'pco', 'PRCOL_00005176' => 'pco', 'Prupe.1G101700' => 'ppe', 'Prupe.5G057500' => 'ppe', 'Prupe.6G219200' => 'ppe', 'Prupe.7G249700' => 'ppe', 'Psat0s679g0120' => 'psa', 'Psat1g023400' => 'psa', 'Psat2g171840' => 'psa', 'PSO017G6169' => 'pso', 'PSO017G6795' => 'pso', 'PSO063G0315' => 'pso', 'PSO170G4997' => 'pso', 'PSO170G6020' => 'pso', 'PSO782G3233' => 'pso', 'QL02p090127' => 'qlo', 'QL02p094256' => 'qlo', 'QL04p043236' => 'qlo', 'QL04p061951' => 'qlo', 'QL04p062534' => 'qlo', 'QL06p039421' => 'qlo', 'QL10p054116' => 'qlo', 'RcHm_v2.0_Chr2g0087501' => 'rch', 'RcHm_v2.0_Chr2g0108351' => 'rch', 'RcHm_v2.0_Chr4g0405431' => 'rch', 'RcHm_v2.0_Chr7g0205491' => 'rch', 'Rhsim03G0251900' => 'rsi', 'Rhsim03G0259600' => 'rsi', 'Rhsim08G0092900' => 'rsi', 'Rhsim10G0126800' => 'rsi', 'Sabra06G0047100' => 'sbr', 'Sabra07G0004100' => 'sbr', 'Sabra14G0005700' => 'sbr', 'Sabra18G0088000' => 'sbr', 'Sabra18G0106200' => 'sbr', 'SalBow1G5510' => 'sbo', 'SalBow1G7837' => 'sbo', 'SalBow6G6150' => 'sbo', 'SalBow6G6170' => 'sbo', 'Sc03g0002440' => 'sci', 'Sc08g0003260' => 'sci', 'Sc08g0003270' => 'sci', 'Sc14g0000130' => 'sci', 'Sed0013868' => 'sed', 'Sed0021397' => 'sed', 'Sed0026414' => 'sed', 'SEGI_37640' => 'sgi', 'SGA_v2.0_scaffold15G07469' => 'sas', 'SGA_v2.0_scaffold233G43598' => 'sas', 'SGA_v2.0_scaffold63G21806' => 'sas', 'SGA_v2.0_scaffold79G25650' => 'sas', 'SHI02831' => 'shi', 'SMO358G0190' => 'smo', 'SMO367G0219' => 'smo', 'Solyc02g092230.3' => 'sly', 'Solyc03g043930.4' => 'sly', 'Solyc07g006020.3' => 'sly', 'Solyc07g007800.3' => 'sly', 'Solyc12g009680.2' => 'sly', 'Solyc12g010480.2' => 'sly', 'Sopen02g036800' => 'spe', 'Sopen07g001090' => 'spe', 'Sopen07g002160' => 'spe', 'Sopen12g004650' => 'spe', 'Sopen12g005490' => 'spe', 'Sp4g03100' => 'spa', 'Sp6g24140' => 'spa', 'Sp7g28730' => 'spa', 'Sp7g35330' => 'spa', 'TAR024G0003' => 'tar', 'TAR026G0003' => 'tar', 'TAR381G0510' => 'tar', 'TAR383G0370' => 'tar', 'TAR626G0112' => 'tar', 'THA.LOC104803554' => 'tha', 'THA.LOC104807634' => 'tha', 'THA.LOC104811022' => 'tha', 'THA.LOC104819901' => 'tha', 'Thecc.01G074100' => 'tca', 'Thecc.09G134100' => 'tca', 'Thecc.09G154500' => 'tca', 'Thhalv10000219m.g' => 'esa', 'Thhalv10014079m.g' => 'esa', 'Thhalv10025325m.g' => 'esa', 'Thhalv10025437m.g' => 'esa', 'TPR.G22031' => 'tpr', 'TPR.G33698' => 'tpr', 'TPR.G7622' => 'tpr', 'TPR.G9334' => 'tpr', 'TPR.G9522' => 'tpr', 'TWI32G0324' => 'twi', 'TWI34G1624' => 'twi', 'TWI39G1053' => 'twi', 'TWI63G1133' => 'twi', 'unitig_52.g17606' => 'ugi', 'unitig_746.g26544' => 'ugi', 'unitig_899.g14425' => 'ugi', 'unitig_899.g14426' => 'ugi', 'vmacro05420' => 'vma', 'vmacro06050' => 'vma', 'vmacro06158' => 'vma', 'vmacro18021' => 'vma', 'VMungo1215G0223' => 'vmu', 'VMungo1215G2930' => 'vmu', 'VMungo1215G3072' => 'vmu', 'VMungo1309G0934' => 'vmu', 'VMungo1309G1801' => 'vmu', 'Zm00001eb007880' => 'zma', 'Zm00001eb009430' => 'zma', 'Zm00001eb206660' => 'zma', 'Zm00001eb233930' => 'zma', 'Zm00001eb264590' => 'zma', 'Zm00001eb388960' => 'zma' ) $gf_id = 'HOM05D001114' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001114' ) $data_identifier = 'HOM05D001114' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 5, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 11, 'ath' => (int) 8, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 10, 'bca' => (int) 19, 'bol' => (int) 9, 'bra' => (int) 9, 'can' => (int) 9, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 6, 'din' => (int) 6, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 11, 'fan' => (int) 15, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 15, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lja' => (int) 4, 'lonja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 6, 'mpo' => (int) 4, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 5, 'oeu' => (int) 8, 'osa' => (int) 7, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 5, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 7, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 4, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb388960' $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